Mutagenetix > Incidental Mutation

Incidental Mutation 'R2133:Lgmn'

233576

Institutional Source

Beutler Lab

Gene Symbol

Lgmn

Ensembl Gene

ENSMUSG00000021190

Gene Name

legumain

Synonyms

Prsc1, preprolegumain, AEP

MMRRC Submission

040136-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2133 (G1)

Quality Score

114

Status

Not validated

Chromosome

Chromosomal Location

102394084-102439813 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 102394908 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 400 (Y400C)

Ref Sequence

ENSEMBL: ENSMUSP00000105647 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021607] [ENSMUST00000056950] [ENSMUST00000110020] [ENSMUST00000133820]

AlphaFold

O89017

Predicted Effect

probably damaging
Transcript: ENSMUST00000021607
AA Change: Y400C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000021607
Gene: ENSMUSG00000021190
AA Change: Y400C

Domain	Start	End	E-Value	Type
low complexity region	5	22	N/A	INTRINSIC
Pfam:Peptidase_C13	31	288	8e-120	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000056950

SMART Domains

Protein: ENSMUSP00000060771
Gene: ENSMUSG00000044456

Domain	Start	End	E-Value	Type
low complexity region	20	32	N/A	INTRINSIC
SH2	61	149	1.89e-2	SMART
low complexity region	254	311	N/A	INTRINSIC
low complexity region	316	325	N/A	INTRINSIC
low complexity region	358	380	N/A	INTRINSIC
low complexity region	448	469	N/A	INTRINSIC
low complexity region	514	523	N/A	INTRINSIC
low complexity region	579	594	N/A	INTRINSIC
low complexity region	714	728	N/A	INTRINSIC
VPS9	736	852	5.75e-38	SMART
RA	873	960	3.5e-4	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000110020
AA Change: Y400C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000105647
Gene: ENSMUSG00000021190
AA Change: Y400C

Domain	Start	End	E-Value	Type
low complexity region	5	22	N/A	INTRINSIC
Pfam:Peptidase_C13	31	288	8e-120	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000133820

SMART Domains

Protein: ENSMUSP00000122646
Gene: ENSMUSG00000044456

Domain	Start	End	E-Value	Type
Blast:SH2	1	69	3e-39	BLAST
SCOP:d1a81a2	3	77	2e-4	SMART
low complexity region	174	231	N/A	INTRINSIC
low complexity region	236	245	N/A	INTRINSIC
low complexity region	278	300	N/A	INTRINSIC
low complexity region	368	389	N/A	INTRINSIC
low complexity region	434	443	N/A	INTRINSIC
low complexity region	499	514	N/A	INTRINSIC
low complexity region	634	648	N/A	INTRINSIC
VPS9	656	772	5.75e-38	SMART
RA	793	880	3.5e-4	SMART

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.3%
20x: 94.9%

Validation Efficiency

MGI Phenotype

FUNCTION: This gene encodes a member of the cysteine peptidase family C13 that plays an important role in the endosome/lysosomal degradation system. The encoded inactive preproprotein undergoes autocatalytic removal of the C-terminal inhibitory propeptide to generate the active endopeptidase that cleaves protein substrates on the C-terminal side of asparagine residues. Mice lacking the encoded protein exhibit defects in the lysosomal processing of proteins resulting in their accumulation in the lysosomes, and develop symptoms resembling hemophagocytic lymphohistiocytosis. [provided by RefSeq, Aug 2016]
PHENOTYPE: Homozygotes for a null allele exhibit slow postnatal weight gain, develop features of hemophagocytic syndrome, and accumulate giant lysosomes in renal tubule cells. Homozygotes for another null allele display impaired TLR9 signaling in dendritic cells, progressive kidney pathology, and proteinuria. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 121 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700067P10Rik	A	G	17: 48,090,452	K86E	possibly damaging	Het
9030624J02Rik	T	C	7: 118,794,575	Y516H	probably damaging	Het
Abcb11	A	T	2: 69,323,883	V113E	possibly damaging	Het
Acacb	TGGGG	TGGG	5: 114,209,767		probably null	Het
Adgrb1	T	A	15: 74,529,908	L251Q	probably damaging	Het
Akap13	G	T	7: 75,611,434	A1269S	probably benign	Het
Aox3	A	G	1: 58,169,843	H845R	probably damaging	Het
Apc	C	A	18: 34,312,045	Q665K	possibly damaging	Het
Atp13a2	T	A	4: 141,005,016	M864K	probably damaging	Het
Atp6v1c2	T	C	12: 17,321,611	T62A	probably benign	Het
Atp7b	T	C	8: 22,011,077	T937A	probably damaging	Het
BC034090	C	T	1: 155,225,786	G244D	probably benign	Het
C2	G	A	17: 34,879,902	T146M	probably damaging	Het
Cacna1h	A	G	17: 25,383,528	F1403L	probably damaging	Het
Camk2b	T	C	11: 5,977,880	E390G	probably benign	Het
Cars	C	A	7: 143,592,474	R71M	probably damaging	Het
Ccdc141	G	A	2: 77,059,607	T447I	probably benign	Het
Cep164	T	C	9: 45,803,183	E182G	probably damaging	Het
Clstn3	T	C	6: 124,449,503	T575A	probably benign	Het
Cntnap2	T	C	6: 47,298,445	L1277P	probably damaging	Het
Cyp4a14	A	T	4: 115,491,391	S325R	probably damaging	Het
Dbt	T	A	3: 116,539,124	D16E	probably damaging	Het
Ddx10	T	A	9: 53,149,512	R768S	probably benign	Het
Dis3	A	T	14: 99,079,877	N710K	probably benign	Het
Dmrta1	A	T	4: 89,688,709	Q134L	probably damaging	Het
Eif3i	A	T	4: 129,596,926	H18Q	probably benign	Het
Emx2	A	G	19: 59,464,033	T250A	probably damaging	Het
Epb41l4a	T	C	18: 33,874,195	T248A	probably damaging	Het
Epm2a	A	G	10: 11,343,682	E71G	probably benign	Het
Eps15l1	A	T	8: 72,386,868	V260D	probably benign	Het
Etv4	A	G	11: 101,775,417	I95T	probably damaging	Het
Etv6	T	C	6: 134,248,754	V316A	possibly damaging	Het
Exoc4	T	C	6: 33,758,158	V570A	probably benign	Het
Exoc4	T	C	6: 33,910,538	S754P	probably benign	Het
Faf1	A	G	4: 109,710,845	N34S	probably damaging	Het
Fam208a	A	G	14: 27,476,614	N1301S	possibly damaging	Het
Fam217a	T	C	13: 34,913,680	H208R	probably damaging	Het
Fgf17	T	C	14: 70,638,487	R102G	probably damaging	Het
Fhad1	G	A	4: 141,928,400	R798C	probably damaging	Het
Fkbp15	C	A	4: 62,327,899	G431W	probably damaging	Het
Gatsl2	G	A	5: 134,136,153	C187Y	probably damaging	Het
Gemin4	G	C	11: 76,211,050	P962A	probably damaging	Het
Gm1587	A	T	14: 77,794,856	C113*	probably null	Het
Gm28040	AGTG	AGTGGCACCTTTGGTG	1: 133,327,321		probably benign	Het
Golim4	A	T	3: 75,908,149	V116D	probably damaging	Het
Gpr132	A	G	12: 112,852,403	S268P	probably damaging	Het
Gtpbp2	T	C	17: 46,161,202	M21T	probably benign	Het
Guca2b	T	C	4: 119,657,631	R78G	probably benign	Het
Helz	T	A	11: 107,670,484	N775K	unknown	Het
Ift20	G	A	11: 78,540,034	E68K	probably damaging	Het
Insrr	G	A	3: 87,810,572		probably null	Het
Ipo9	ATCCTCCTCCTCCTCCTC	ATCCTCCTCCTCCTCCTCCTC	1: 135,386,268		probably benign	Het
Ipo9	TCC	TCCACC	1: 135,386,275		probably benign	Het
Ipo9	A	G	1: 135,402,250	V484A	probably benign	Het
Irak3	A	G	10: 120,165,177	I281T	probably benign	Het
Kcnh8	T	C	17: 52,893,933	V465A	probably damaging	Het
Khsrp	A	T	17: 57,027,832	I138N	probably benign	Het
Larp1b	T	C	3: 40,970,535	M149T	possibly damaging	Het
Ldhc	A	T	7: 46,869,599	D82V	probably damaging	Het
Lmo2	T	C	2: 103,981,062	Y147H	probably damaging	Het
Lmtk2	C	T	5: 144,174,988	T842I	possibly damaging	Het
Lpo	T	A	11: 87,821,130	I34F	probably benign	Het
Magel2	A	T	7: 62,377,738	H130L	unknown	Het
Mamld1	C	A	X: 71,119,392	Q670K	probably benign	Het
Mcrs1	A	T	15: 99,243,375	D402E	probably damaging	Het
Mki67	T	A	7: 135,704,241		probably null	Het
Morc2a	T	A	11: 3,680,302	C499*	probably null	Het
Mpp2	G	A	11: 102,064,595	R110C	probably benign	Het
Msra	T	A	14: 64,233,928	T47S	probably damaging	Het
Nrp1	A	T	8: 128,498,516	E782D	probably damaging	Het
Ogdhl	T	C	14: 32,325,934	V47A	probably benign	Het
Olfml3	T	A	3: 103,735,869	M399L	probably benign	Het
Olfr1245	G	A	2: 89,575,256	Q157*	probably null	Het
Olfr341	A	G	2: 36,480,047	S28P	possibly damaging	Het
Olfr453	C	A	6: 42,744,135	L33M	possibly damaging	Het
Optc	A	T	1: 133,903,796		probably null	Het
Osbpl6	T	A	2: 76,586,214	I546K	probably damaging	Het
Pard6g	T	C	18: 80,117,308	V212A	probably damaging	Het
Pcdhb14	C	A	18: 37,447,870	Q10K	probably benign	Het
Pkhd1l1	T	C	15: 44,516,185	I1069T	possibly damaging	Het
Plcb1	T	A	2: 135,325,667	Y460*	probably null	Het
Plekha6	C	A	1: 133,279,365		probably null	Het
Prelp	C	T	1: 133,915,131	R92K	probably benign	Het
Ptprg	T	A	14: 12,211,637	I198N	probably damaging	Het
Rbm12	A	T	2: 156,095,510	C947*	probably null	Het
Rc3h2	A	T	2: 37,378,916	I846K	probably benign	Het
Ren1	C	A	1: 133,358,982		probably null	Het
Rfwd3	A	T	8: 111,297,402	V96E	probably benign	Het
Rnf157	A	G	11: 116,358,694	V232A	possibly damaging	Het
Ror1	A	G	4: 100,410,025	N308D	probably benign	Het
Rrp1	T	C	10: 78,401,894		probably benign	Het
Rsph6a	T	A	7: 19,068,106	V360E	probably damaging	Het
Senp1	T	A	15: 98,075,967	T132S	probably benign	Het
Sept4	A	T	11: 87,583,436	Q60L	probably benign	Het
Slc41a3	C	T	6: 90,626,381	A128V	probably damaging	Het
Slc7a9	T	C	7: 35,453,493	F112S	probably damaging	Het
Slc9a4	T	G	1: 40,607,741		probably null	Het
Sort1	T	A	3: 108,351,686	F678Y	probably benign	Het
Spidr	G	A	16: 16,053,273	L278F	probably benign	Het
Stard13	T	C	5: 151,045,168	Y879C	probably damaging	Het
Synpo	T	C	18: 60,602,895	N421D	probably damaging	Het
Syt17	C	T	7: 118,382,047	G351S	possibly damaging	Het
Tacc1	A	T	8: 25,164,493	N271K	probably damaging	Het
Tdrd6	T	C	17: 43,624,833	T1775A	probably benign	Het
Tecpr1	T	A	5: 144,208,645	T595S	probably benign	Het
Tjp3	T	A	10: 81,278,054	M457L	possibly damaging	Het
Tmem132a	C	A	19: 10,864,066	R298L	probably benign	Het
Trabd2b	A	T	4: 114,610,008	Q478L	probably benign	Het
Trappc12	A	T	12: 28,746,598	S312T	probably benign	Het
Trove2	T	C	1: 143,760,034	D458G	probably benign	Het
Ttc9b	T	A	7: 27,654,349		probably null	Het
Ttn	G	A	2: 76,850,612	Q1044*	probably null	Het
Ugt2b34	C	T	5: 86,906,557	D122N	probably benign	Het
Zc3h6	A	G	2: 128,967,830	H9R	possibly damaging	Het
Zdhhc13	T	A	7: 48,824,644	L548Q	possibly damaging	Het
Zfp236	T	C	18: 82,621,304	M1225V	probably benign	Het
Zfp280d	T	C	9: 72,308,005	F133L	probably damaging	Het
Zfp521	G	A	18: 13,844,705	P884S	possibly damaging	Het
Zfp64	A	G	2: 168,940,743	Y146H	probably damaging	Het
Zfyve26	T	A	12: 79,268,434	I1423F	possibly damaging	Het
Zswim6	T	A	13: 107,743,987		noncoding transcript	Het

Other mutations in Lgmn

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00823:Lgmn	APN	12	102398176	splice site	probably benign
IGL02069:Lgmn	APN	12	102404299	missense	possibly damaging	0.92
IGL02150:Lgmn	APN	12	102395727	missense	possibly damaging	0.80
IGL02228:Lgmn	APN	12	102395714	missense	probably benign	0.04
IGL02637:Lgmn	APN	12	102400226	missense	probably damaging	0.98
Getz	UTSW	12	102399989	missense	probably damaging	0.99
R0233:Lgmn	UTSW	12	102399989	missense	probably damaging	0.99
R0233:Lgmn	UTSW	12	102399989	missense	probably damaging	0.99
R0988:Lgmn	UTSW	12	102398277	missense	probably damaging	0.99
R1451:Lgmn	UTSW	12	102405892	splice site	probably benign
R1568:Lgmn	UTSW	12	102394609	missense	possibly damaging	0.95
R1944:Lgmn	UTSW	12	102401924	missense	probably damaging	1.00
R1972:Lgmn	UTSW	12	102395821	unclassified	probably benign
R2298:Lgmn	UTSW	12	102395678	missense	probably damaging	0.99
R3846:Lgmn	UTSW	12	102404329	missense	possibly damaging	0.87
R4610:Lgmn	UTSW	12	102400124	splice site	probably benign
R4788:Lgmn	UTSW	12	102402677	missense	probably benign	0.11
R5050:Lgmn	UTSW	12	102403421	splice site	probably null
R5708:Lgmn	UTSW	12	102404328	missense	possibly damaging	0.87
R5969:Lgmn	UTSW	12	102405827	missense	probably damaging	1.00
R6090:Lgmn	UTSW	12	102400154	missense	probably damaging	1.00
R6420:Lgmn	UTSW	12	102423719	nonsense	probably null
R6496:Lgmn	UTSW	12	102398239	missense	probably benign	0.01
R6592:Lgmn	UTSW	12	102404270	missense	probably damaging	1.00
R6659:Lgmn	UTSW	12	102402692	missense	probably benign	0.03
R7063:Lgmn	UTSW	12	102402678	missense	probably damaging	1.00
R7336:Lgmn	UTSW	12	102423739	start gained	probably benign

Predicted Primers

PCR Primer
(F):5'- TGAGTGGCCTCAGGAACTACAG -3'
(R):5'- GTTCCCAGAATCAGCTGAAGC -3'

Sequencing Primer
(F):5'- TCAGGAACTACAGTCTCCTCAGG -3'
(R):5'- TGGACAGAGTTTCAGCAGCC -3'

Posted On

2014-10-01